MineICA (version 1.12.0)

selectWitnessGenes: selectWitnessGenes

Description

This function selects a gene per component.

Usage

selectWitnessGenes(icaSet, params, level = c("genes", "features"), maxNbOcc = 1, selectionByComp = NULL)

Arguments

icaSet

An object of class IcaSet

params

An object of class MineICAParams containing the parameters of the analysis, the attribute cutoffSel is used as the threshold.

level

The attribute of icaSet to be used, the witness elements will be either selected within the "features" or the "genes"

maxNbOcc

The maximum number of components where the genes can have an absolute projection value higher than cutoffSel(params) in order to be selected.

selectionByComp

The list of components already restricted to the contributing genes

Value

This function returns a vector of IDs.

Details

Selects as feature/gene witness, for each component, the first gene whose absolute projection is greater than a given threshold in at the most maxNbOcc components. These witnesses can then be used as representatives of the expression behavior of the contributing genes of the components.

When a feature/gene respecting the given constraints is not found, maxNbOcc is incremented of one until a gene is found.

Examples

## load an example of IcaSet
data(icaSetCarbayo)

## define parameters: features or genes are considered to be contributor
# when their absolute projection value exceeds a threshold of 4.
params <- buildMineICAParams(resPath="carbayo/", selCutoff=4)

## selection, as gene witnesses, of the genes whose absolute projection is greater than 4
# in at the most one component. I.e, a gene is selected as a gene witness of a component
# if he has a large projection on this component only.
selectWitnessGenes(icaSet=icaSetCarbayo, params=params, level="genes", maxNbOcc=1)

## selection, as gene witnesses, of the genes whose absolute projection is greater than 4
# in at the most two components.
# I.e, a gene is selected as a gene witness of a given component if he has a large projection
# in this component and at the most another.
selectWitnessGenes(icaSet=icaSetCarbayo, params=params, level="genes", maxNbOcc=2)